I'm presently trying to map out Nyx's progression through the story. This is something which isn't so much a part of the plot as it is a character development. The readers need to see Nyx changing as the story moves forward. The story transforms her so much, but it needs to do so carefully and deliberately. The reader should be able to watch this unfold in a realistic and gradual way.

So, I've divided my notes into three sections on this topic. First, we have general alicorn transformation. Second, we have Nyx's specific abilities. Third, we have Nyx's moral struggles.

Alicorn Transformation Order:

1. The alicorn's horn throughput momentarily and dramatically increases as it develops the mechanisms to wield the massive power of the Aether. This does not access the Aether at this stage, but it produces a burst of magical ability far in excess of what a mortal unicorn should be able to achieve. This is marked with the phenomenon of draining external power sources if the alicorn should burn out. What is going on is the horn is beginning to expect that unlimited pool of power of the Aether, but it is not yet matured enough to tap it. If the local Lifestream does not have enough to supply the spell, nearby ponies may be tapped as well. Unicorns would involuntarily contribute their energy toward the spell, possibly burning them out as well.

2. Nightmares would occur, tempting the alicorn to take refuge in a new identity as a wild alicorn. They will try to convince the alicorn that staying the way they are is not safe. This temptation will persist and increase over time, and eventually invade the waking state in addition to the nightmares. The temptation feels alien at first, suggesting the alicorn embrace something they do not consider normal or valid. Over time, the alicorn will become confused as to which is correct, and ultimately, their former identity will be the one which feels alien. This back and forth struggle will be affected by how much the alicorn resists it. And resisting it always involves embracing mortal pony virtues. The more the alicorn values the lives of mortal ponies, the longer they can hold out resisting the transformation.

3. The alicorn's horn will briefly tap into the Aether. This may only be for a very brief moment, but it will be recognizable in that excessive energy is used which does not deplete their internal reserves. This happens during times of high stress or urgency. In chapter 3, Luna should ask Nyx about the device on her foreleg, and whether she noticed any energy drop after burning the zebras. Nyx would have a habit at this time of checking it often during a fight because she can't afford to burn out.

4. New skills are developed which utilize the Aether. This could be something profound but highly specific such as Celestia learning to move the sun. These skills are not lost if the transformation is halted.

5. The alicorn's overall physical strength will increase, allowing them to take even more punishment without risk of harm. They will become more proficient in combat as well.

6. The alicorn's moral degradation would progress, making it difficult to see what is important. They would stop "caring" as much, becoming indifferent and perhaps having a form of amnesia where they temporarily forget key moments in their lives which connected them to others in a meaningful way.

7. The alicorn will view themselves as superior to mortal ponies in every way. They will challenge authority, and make up their own rules. They will take action without consulting others, and put others' lives at risk to further their own agenda.

8. The alicorn will gain mastery over the Aether, utilizing it to their will. At this stage, the transformation is likely irreversible.

9. The alicorn will fully abandon ties with the mortals, forging their own path separate from them. They will cease viewing the mortals as "people" and forget that they were once like them.

10. The alicorn will either view the mortals as an annoyance or as a form of amusement. Neither would go well for the mortals. At this stage, the alicorn is a demigod existing in the same world as mortals. Every action they do can potentially kill untold numbers. The mortals learn that their only choice is to try and avoid the alicorn at all costs.

11. The alicorn eventually becomes nihilistic and potentially depressed to the point of suicide or leaving the world forever via the Aether in search of more interesting things.

Nyx's Abilities:

1. At the start of the story, Nyx has already reached stages 1 and 2 of the alicorn transformation. In chapter one, she reaches stage 3 with the burning of the zebra sniper squad. Her abilities at this point are impressive by mortal pony standards, but they are not widely varied, nor significantly useful in the big picture of the world. Nyx is a superior fighter despite her lack of experience. She is physically much stronger than mortals, and always has been. Her shield is stronger than a typical unicorn's, but not by much. She has a horn weapon like most unicorns which has a concussive blast, but she also has a cutting beam which uses much more energy. Nyx's mastery of levitated weapons is decent, and at least on par with a trained unicorn sword fighter. One of Nyx's main problems at this stage is that her overall energy capacity is relatively low, and it recharges from the Lifestream at a rather unimpressive rate similar to the rate of an average unicorn.

2. Nyx will be gaining efficiency about the time of the next battle. This will give her much more staying power in combat.

3. Celestia will take the time to teach Nyx some war magic. She has tapped into the Aether again momentarily by this time, and Celestia wants her to gain control over it rather than being impulsive. It is stressed that Nyx needs to not waste time in connecting with her virtue. The sisters discuss the possibility of using the Elements of Harmony against her, should she show signs of being close to an irreversible transformation.

4. Luna teaches Nyx how to use her dreamwalking abilities. Nyx has momentarily reached into the dreams of others, but never in a way she could control herself. Luna also helps Nyx learn to consciously tap the Aether for a task rather than relying on her internal reserves from the Lifestream. The Aether does not use internal reserves. It is always the alicorn's horn channeling energy directly from the Aether.

5. Nyx will apply what she has learned to some creative new abilities, yet to be decided.

Nyx's Moral Struggles:

1. Nyx struggles with her nightmares and the fear that they are tempting her to become something she doesn't want to be. Nyx is currently timid, insecure, and claustrophobic. She is emotionally oversensitive and still attached to her past experience as a victim.

2. The incident where she burned the zebra sniper squad was troubling to her, but she did not have much time to dwell on it before being put on her mission.

3. Regret over the failure to save Lily. This was Nyx's second attempt at heroism in a week's time, but it did not go so well as it did last time. She's got a lot of feelings of guilt over it.

4. Nyx kills her first infected pony. It doesn't help that she does this with a tap from the Aether. Nyx is horrified at the fact that she has killed a pony for the first time. She swore to protect ponies, not kill them.

5. Nyx nearly kills a pony she mistakes for being infected. She wounds the pony, and then upon seeing that they felt pain and fear, she relented before dealing the killing strike.

6. Nyx kills Sage. This would be terrible for her, as all along, she has been trying to support and restore that family. Being the instrument of death to Sage would be devastating for her.

7. Several times in the second act, Nyx would struggle with the seemingly pointless nature of the pony/zebra war. She would begin to wonder if the things ponies suffered were just a symptom of their weakness as a species, and that perhaps this was just nature taking its course.

8. Nyx directly challenges Luna and Celestia's authority. She views them as closer to mortals than to true alicorns. She demonstrates that she is physically superior to them without truly harming them, just to show them their place relative to her.

9. Nyx's climax in her internal struggle is when she is watching the great battle from up in a cloud. The battle rages below her between innumerable ponies and zebras, and the ponies seem to be losing their ground. Nyx seriously considers giving up the fight as meaningless. She wonders why it matters, and why she fights for them. She recalls Rumble's undying love for her though, and realizes that there are definitely aspects of the mortal ponies which are worth fighting for. This is the moment where she makes the decision that she will choose to fight and to keep her vow to protect. She races down and engages the battle, pushing the balance enough that the ponies are able to repel the invaders.

It is important to note that between each of these stages, Nyx reverts back to her "normal" self. These are but momentary struggles for Nyx, as she fights against her transformation. Each instance is more severe than the last, but she fights it off each time, remembering the love and support of her family, which keeps her grounded.

Continued in this post below.

4743929
It's a nice blend of natural instincts, temptation and morale degradation. It's also subtle, there's no, to use a star wars anaology "hey join the dark side? Umm okay.." moment. Best part is, the war is itself pushing Nyx which is a nice factor.

Having the "moments" brief also cam trick the reader into thinking its something else, stress, depression etc which makes it even better

4744025
Yeah, I despise sudden commitments to evil for "Reasons". Ugh. No, Nyx's progression needs to be gradual, but also plausible. And I also despise lengthy periods of time where the hero is acting like a villain. It's just difficult for me to stomach. When Nihilus took over Twilight, I simply couldn't wait for it to be over. I'm not going to do that to Nyx. Her moments of moral confusion will be exactly that: Moments. This is meant to demonstrate how the power of a loving family can and does cleanse and strengthen someone's moral fortitude. That's one theme I really want to drive home in this story.

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Part of me felt the book lost some of its impact once Nihilius was defeated, having friends face off against one of their own has a lot more dramatic impact. That said, Nihilius wasn't the greatest bad girl that she could've been; something was missing from her that I couldn't quite put my finger on. I guess she just felt petty somehow, hating Twilights friends just because she was made that way as opposed to having a genuine reason.
That and Twilight became the greatest genius magician that ever lived

But anyway, You're onto the good stuff regarding Nyx's progression, brief moments of distorted morality make far more sense than "grrr something bad happened! I'm in a homicidal rage!" It's far more natural, everyone has moments of weakness and it's good that her friends and loved ones are what are keeping her centred.

4744584
Oh, Nihilus was certainly dramatic and created heaps of tension, I agree. But I think it was for all the wrong reasons. I felt tense for certain. But it was the kind of tension that isn't enjoyable, at least to me. I just wanted it to be over so they could address the real problem that was nagging at me, which was simply ignored for 100k words. Teasing the reader with stuff like "Is Celestia even still alive" and all that is a poor tease because it's a safe bet that she is still alive, but knowing all the characters believe otherwise is an awkward feeling because we the readers are privy to info that none of the heroes are aware of. Moreso, again, I hate when the hero acts like a villain for extended time. It was made worse by the fact that it wasn't for any good reason than "by decree". Nihilus was created to be the anti-Twilight. Even she didn't know why she hated the way she did. Another thing which seriously bothered me was the willy nilly "balance of power" problems, such as Luna (an alicorn) getting full-on spanked by Nihilus, multiple times, even with the established premise that... "the weakest alicorn can take the strongest unicorn". Really? That makes Luna look pretty damn pathetic. But yeah. These plausibility and consistency problems are the precise reason why I'm spending time actually taking care of this stuff in advance. I don't want to fall into the same mistakes.

In real life, people fall into morality problems gradually. It's like the progression of an addict. It's slow at first, and then slowly creeps in and takes over your life. Most people are rational and intelligent enough that if the full effect happened immediately, they would recoil and reject it. Nobody just "flips" without going through a gradual progressive degeneration. Well maybe some people do in extreme enough situations. But I wager that even those people were building it up for a while before they just snapped.

everyone has moments of weakness

And this is a central part of good storytelling, I think. Making the actions of your characters relatable to the common person. Weaknesses "everyone has" are the best weaknesses to portray in a story. Look at the success of MLP itself. Here, we have magical, talking, candy-colored horses having the exact same types of conflicts that real people have all the time! That is what makes the show so relatable. The fact that they are in a fantasy universe and are ponies helps us ignore the fact that we're looking at depictions of real people, and keeps that part of our brain which seeks something different engaged while connecting with that part of our brain which expects something relatable. Or, as AntonyC put it in his Fo:E comments,

What's really tickled my fancy about it is the always fascinating concept of sticking cute animal-people in heinous grown-up situations. I think the disconnect between that familiar contempt we feel for our own species and the love we have for innocent animals gives us an interesting vantage point from which to view such a story with its grimness, despair, and sexual confusion. Lo, when it's given life by a cast of adorable ponies who are innately impossible to dismiss with the same disappointment one feels for one's own kind.

My point being that it is a perfect combination of great fantasy storytelling and realistic portrayal of conflict that makes it work. When you have characters interact and behave in an unrelatable manner, then the reader is likely (hopefully) to lose interest.

4744962
Yeah, Luna get's her flank absolutely spanked in almost every fight she's in, they give the excuse that her exile to her moon stopped her maturing at the same level as Celestia. But its a pretty poor showing for moon butt, she seems to be in even Twilights shadow, but then that was Celestias plan all along. Even Lunas supposed skill with a blade never really got a good showing she always faced off against superior opponents but then Luna is best pony to me,

It's a really interesting take on morality and how we perceive it as human beings, through the eyes of a cartoon pony that are innocent and pure, yet are thrown into terrible situations. Peri and Nyx make an interesting moral duo, you have a goddess that stood against the monster her husband had become to protect ponies she barely knew, and you have Nyx, a creation that is trying to find her own identity and values and protect the ponies she's grown to love. It's a credit to you that you've made lot's of relatable characters already.

One interesting thing that just came to me, when Nyx challenges Luna and Celestia it would also be over their impotence as supposed protectors of ponies, they've allowed a war to unfold and have done nothing while innocent ponies have died. Given what Nyx has gone through by that point she'd be feeling such bitterness regarding what she's had to do.

when Nyx challenges Luna and Celestia it would also be over their impotence as supposed protectors of ponies, they've allowed a war to unfold and have done nothing while innocent ponies have died.

Yep, that's perfect actually. A great catalyst for Nyx to view them as failures for a moment.

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Alright, I've identified six key moments in the story where Nyx has what I'll call a "moral lapse". This is when she has an episode which causes her to lose track of her moral center for a moment. The idea is that these increase in severity over time as we approach the climax of the story.

The cause of the moral lapse is her transformation into a wild alicorn. It is in her biology. It is not caused by the Aether. A key identifiable characteristic of these moments is that Nyx noticeably behaves more like Nightmare Moon would behave, since Nightmare Moon is literally Nyx as a wild alicorn. [edit] Not quite, but close enough, I suppose.

So, here we go:

1 - The Sniper Attack.
When Nyx saves Dusty from the snipers, she is furious. She races toward the two remaining zebra soldiers intending to confront and capture them - battle them if necessary. Once she arrives, she has an episode just for a moment where she taps the Aether and incinerates them. She gives them no quarter, which is a key trait of Nightmare Moon. The moment ends almost immediately, and she breaks down and weeps. She did not intend to burn them alive, but for that brief moment, she was not herself.

2 - The Battle of Withersberg.

Nyx's moral lapse is that she begins to engage the infected ponies with no quarter. She starts slaying them as animals to be put down, forgetting her previous hesitation and internal struggle that "they are ponies", contradicting her vow to protect them.

As it turns out, this actually helps the situation because Nyx is a better fighter at a time when she really needs to be. The problem is that she is not using proper discretion with her targets. She nearly kills a pony she mistakes for being infected. She notices the fear and pain which signify that this is not an infected pony, but she does not process the information quick enough. Rumble intervenes, stopping her from the killing blow.

Also, Nyx kills Sage in a fit of anger. She pauses before killing him, recognizing who it is. He attacks her with knives, cutting her leg. She takes his head off and moves on. After the battle, Nyx comes down off her moral lapse and is devastated by what she has done.

3 - Nyx and her team clean the 2nd nest after Withersberg.

Nyx's moral lapse here is that she begins to wonder if the things ponies are suffering are just symptoms of their weakness as a species, and that perhaps this is just nature taking its course. Perhaps Nyx looks at the dead and isn't bothered. Maybe she kicks a severed head and watches it roll away, contemplating that mortal pony lives are so fleeting anyway. It is in their very nature to die, so is this really so horrible?

Her friends would be appalled at this, but she would argue that this whole war doesn't make any sense. That it's just so petty, and maybe they are all stressed out over it for no reason. Naturally, her friends would disagree, and they would appeal to Nyx's sense of love and loyalty to her fellow ponies. She would at first say that she's not like other ponies. But they would recall some meaningful parts from Nyx's childhood. And Nyx would not remember them.

She would storm off to be alone for a while. Rumble would want to follow, but Flitter would tell him to give her a moment. Nyx would walk back to give them some more of the same, and suddenly she would recover from her episode and not understand anything that's going on. She would be confused and feel terrible for having said such awful things. Rumble would ask if she remembered that moment from her childhood, and she would recall it, where moments before she couldn't. Nyx would feel frightened about what is happening to her, that she is not being herself. She doesn't want to be the pony that she was a moment ago, but it just... happens.

This would be an important episode in that it is not connected with any sort of violence. It's just Nyx losing herself for a little bit and coming back. A symptom of what is to come.

4 - Terrorizing zebras

This episode happens when the rest of the team is returning from extracting Zecora's sister from the zebra nation.

Nyx's moral lapse here is that she sees Zecora's sister, who is very nervous at the sight of Nyx.
Nyx takes amusement at this. She pretends to be Nightmare Moon for a moment to deliberately freak the zebra out.

Maybe she just got back from taking a walk through Zebratown, pondering the difference between pony and zebra lives, and whether one is worth more than the other. The zebras are terrified of her. She says "You are right to fear me, mortal." She snaps her teeth at them, grins, and flies off.

This would be highly uncharacteristic of Nyx, being malicious and bullying toward someone. Unfortunately, she will have to go back and apologize.

5 - Confronting the Royal Sisters

This is after Nyx gets the crystal from the dead tree.
Nyx asks for the rest of the story about Everfree. She's upset that the sisters have held out important information from her.
Luna asks to see the crystal. Breaks down emotionally because it's all that remains of her mother and she hasn't seen it in over five thousand years
Nyx softens, listening to Luna and Celestia tell the rest of the story from their youth. Nyx realizes that these things are truly significant, where the present moment with the zebra war is ridiculous and petty.

Nyx confronts Luna and Celestia about their leadership and their weakness.

Nyx directly challenges Luna and Celestia's authority. She views them as closer to mortals than to true alicorns. She could hold them both up against a wall, accusing them of leading their people into a genocidal war, demanding to know why they don't fight. Saying that they are not worthy to lead the mortals.

Nyx would take on a truly menacing tone here, behaving exactly like Nightmare Moon would.

She would look at Luna, saying "You're weak. Just as you were a thousand years ago when we first met. Do you not remember when you came to me to ease your pain?" Nyx runs her hoof through Luna's mane. "Your mane was such a pretty shade of periwinkle."

Luna would be shocked and terrified. "You shouldn't remember that!"

After a tense moment when it looks like she might do something really terrible, Nyx would then fight off the feeling, collapsing to the floor in tears. She would beg their forgiveness.

Luna would tell her that this will only get worse. That one day, she won't come back.

This would be a good time for Luna to give the crystal to Nyx. It would bond with her armor and give Luna hope that maybe this could end well.

6 - The Battle for Baltimare

This would be a known zebra formation attack pushing toward Baltimare, a heavily populated Equestrian city. If the zebras succeeded, it could mean a million ponies dead. A huge army is mustered, and Nyx is asked to come fight.

Shortly after they enter the fight, Nyx starts showing what a genuine wild alicorn might do in battle. Not to the scale that Hyperion would, but she begins utilizing a scary amount of power. This was a burst, though. A momentary flood of access to the Aether as Nyx's horn matures just a bit more. It is not to be confused with Nyx's learned abilities associated with the Aether.

This battle is intense, and the zebras are pushing very hard with more advanced weapons and better armor. The ponies have adapted as well, increasing their fighting capacity. But they are still being pushed back.

A random zebra scores a solid hit against Nyx. It hurts, but she is fine. She's pissed though, and she stops to ask herself what the hell she's doing in this fight. Nyx flies up high to get perspective on the whole scene.

Nyx has reached the apex of her self-doubt, having progressed toward her "wild alicorn" transformation and gained quite a bit of strength, but also her moral foundation has become fairly shaky. She begins to wonder why she should be fighting for the ponies, or even be associated with them.

Nyx flies up to a cloud and watches the battle rage from a distance. She begins to feel that the entire conflict is beneath her. That the outcome does not matter. She struggles to remember the value of pony lives.

Rumble flies up to talk to her. He's needed on the ground, but he is very concerned for Nyx. He asks why she's not helping. She responds with "Why should I? This whole thing is insignificant. Even you are ultimately insignificant." This stings Rumble, He tells Nyx that he loves her, and he hopes she comes back soon, because they all need her. He flies back down to rejoin the fight.

She goes back to watching the battle from her cloud. She thinks about Rumble and his foolishness. She considers his fierce love for her and wonders why he cares for her so much. Does he worship her? What is his real motive? Love? What is love? Is it a feeling, or is it an action? Is she, an alicorn who is superior to all creatures in every way, superior to Rumble when it comes to love? She has to admit, she is not.

Nyx remembers that love is serving others and putting others first. Protecting others. She snaps out of her final moral lapse and races down to rejoin the fight. There are way too many zebras for even Nyx to make a difference with. She attacks artillery installations which are lobbing balefire eggs into the pony army. She spots key zebra commanders on the battlefield and engages them, taking them out. The decapitated zebra army stumbles about in confusion without orders, and is overwhelmed by pony forces. Those who survive make a hasty retreat.

[edit]
When Nyx has one of these moments where she temporarily has access to the aether and loses touch with her current identity, that would be a great time for her to remember specific events from the past. She could remember most anything from Luna's history or her own, such as when she killed Sombra.

4748689
I like where this is going, it gels well with adolescence and growing up, rebelling against that which you feel holds you back. Immortality, power and war make potent forces of change.

There's a nice slow erosion of Nyx's perception of those around her. As her abilities increase and she's forced to kill, everyponies value diminishes in her eyes, especially when faced with the infected. The fragility of life, especially when she worked so hard to save it would become an irritance and fuel her disconnection. Makes it cool because the war itself becomes a character thats trying to destroy her.

I like how Nightmare Moon takes prominence and how her habit for pranks takes on a far more sinister air. They fear her and she likes it.

Rumble deserves to be the final moment of her spiral, his connection to her is the strongest. You could twist this disconnection by adding a hint of jealousy. He devotes himself to others and not her alone, isn't she their better after all? The fact she realises that true love is selfless is going to be a powerful moment, especially considering the build up leading to her realisation.